Multiplatform molecular analyses refine classification of gliomas arising in patients with neurofibromatosis type 1

Abstract

Gliomas arising in the setting of neurofibromatosis type 1 (NF1) are heterogeneous, occurring from childhood through adulthood, can be histologically low-grade or high-grade, and follow an indolent or aggressive clinical course. Comprehensive profiling of genetic alterations beyond NF1 inactivation and epigenetic classification of these tumors remain limited. Through next-generation sequencing, copy number analysis, and DNA methylation profiling of gliomas from 47 NF1 patients, we identified 2 molecular subgroups of NF1-associated gliomas. The first harbored biallelic NF1 inactivation only, occurred primarily during childhood, followed a more indolent clinical course, and had a unique epigenetic signature for which we propose the terminology "pilocytic astrocytoma, arising in the setting of NF1". The second subgroup harbored additional oncogenic alterations including CDKN2A homozygous deletion and ATRX mutation, occurred primarily during adulthood, followed a more aggressive clinical course, and was epigenetically diverse, with most tumors aligning with either high-grade astrocytoma with piloid features or various subclasses of IDH-wildtype glioblastoma. Several patients were treated with small molecule MEK inhibitors that resulted in stable disease or tumor regression when used as a single agent, but only in the context of those tumors with NF1 inactivation lacking additional oncogenic alterations. Together, these findings highlight recurrently altered pathways in NF1-associated gliomas and help inform targeted therapeutic strategies for this patient population.

Keywords: Astrocytoma; Brain tumor; Glioma; Molecular neuro-oncology; Molecular neuropathology; NF1; Neurofibromatosis type 1; Selumetinib; Trametinib.

Fig. 1

a Oncoprint table summarizing the clinical characteristics, histologic features, DNA methylation cluster assignments, genetic alterations, and chromosomal copy number aberrations identified in the 47 gliomas arising in patients with neurofibromatosis type 1. b Germline and somatic NF1 gene mutations identified in the 47 gliomas arising in patients with neurofibromatosis type 1

Fig. 2

Imaging and histologic features of gliomas arising in patients with neurofibromatosis type 1. a Pilocytic astrocytoma, NF1-associated. b High-grade astrocytoma with piloid features, NF1-associated. c Glioblastoma, NF1-associated

Fig. 2

Imaging and histologic features of gliomas arising in patients with neurofibromatosis type 1. a Pilocytic astrocytoma, NF1-associated. b High-grade astrocytoma with piloid features, NF1-associated. c Glioblastoma, NF1-associated

Fig. 3

Kaplan–Meier curves comparing glioma-specific survival (a) and progression-free survival (b) for the 47 NF1 patients stratified by molecular low-grade versus high-grade groups

Fig. 4

Clinical outcomes for patients with NF1-associated gliomas treated with MEK inhibitors. Swimmer’s plot (top) showing treatment course and clinical outcomes for nine NF1-associated glioma patients whose treatment included either trametinib or selumetinib. Imaging (bottom) demonstrating tumor regression for patient #3 and stable disease for patient #34 while on MEK inhibitor therapy

Fig. 5

DNA methylation clustering analysis of 32 NF1-associated gliomas (black triangles), alongside a reference set of CNS tumor samples (circles). Shown is a two-dimensional representation of pairwise sample correlations using the 35,000 most variably methylated probes using t-distributed stochastic neighbor embedding (tSNE). Reference methylation classes depicted include: CHGL, chordoid glioma; DHG, G34, diffuse hemispheric glioma, H3 G34-mutant; DIG/DIA, desmoplastic infantile ganglioglioma/astrocytoma; DLGNT, diffuse leptomeningeal glioneuronal tumor; DMG, K27, diffuse midline glioma, H3 K27-altered; DNT, dysembryoplastic neuroepithelial tumor; EVN, extraventricular neurocytoma; GBM, MES, IDH-wildtype glioblastoma, mesenchymal subtype; GBM, MID, IDH-wildtype glioblastoma, midline subclass; GBM, MYCN, IDH-wildtype glioblastoma, MYCN subclass; GBM, RTK I IDH-wildtype glioblastoma, RTK I subclass; GBM, RTK II, IDH-wildtype glioblastoma, RTK II subclass; GBM, RTK III, IDH-wildtype glioblastoma, RTK III subclass; GG, ganglioglioma; HGAP, high-grade astrocytoma with piloid features; IHG, infant-type hemispheric glioma; LGG, MYB, low-grade glioma with MYB or MYBL1 rearrangement; PA, MID, midline pilocytic astrocytoma; PA, PF, posterior fossa pilocytic astrocytoma; PA, ST, supratentorial/hemispheric pilocytic astrocytoma; PXA, pleomorphic xanthoastrocytoma; RGNT, rosette-forming glioneuronal tumor; SEGA, subependymal giant cell astrocytoma. See Supplementary Fig. 4 [Online Resource 2] for expanded tSNE plot and Supplementary Table 3 [Online Resource 1] for the sample manifest

Fig. 6

Longitudinal genomic analysis of gliomas arising in the setting of NF1. Shown are genetic evolution dendrograms generated from genomic analysis performed on two temporally or spatially distinct tumor specimens for each of three NF1 patients

Fig. 7

Graphical summary of the three main epigenetic classes of gliomas arising in the setting of neurofibromatosis type 1. PA, pilocytic astrocytoma. GG, ganglioglioma. DA, diffuse astrocytoma. APA, anaplastic pilocytic astrocytoma. HGA, high-grade astrocytoma. GSS, glioma-specific survival. PFS, progression-free survival